On the Search for Retrotransposons: Alternative Protocols to Obtain Sequences to Learn Profile Hidden Markov Models

Autor(es)

Fischer, Carlos N. ^[1] ; Campos, Victor De A. ^[2] ; Barella, Victor H. ^[3]

Afiliação do(s) autor(es)

^[1] UNESP Sao Paulo State Univ, Dept Stat Appl Maths & Comp Sci, Ave 24-A, 1515, BR-13506900 Rio Claro, SP - Brazil

^[2] UNESP Sao Paulo State Univ, Inst Biosci, Dept Comp Sci, Sao Jose Do Rio Preto - Brazil

^[3] Univ Sao Paulo, Inst Math & Comp Sci, Dept Comp Sci, Sao Carlos, SP - Brazil

• Tipo de documento: Artigo Científico
• Fonte: JOURNAL OF COMPUTATIONAL BIOLOGY; v. 25, n. 5, p. 517-527, MAY 2018.
• Citações Web of Science: 1

Resumo

Profile hidden Markov models (pHMMs) have been used to search for transposable elements (TEs) in genomes. For the learning of pHMMs aimed to search for TEs of the retrotransposon class, the conventional protocol is to use the whole internal nucleotide portions of these elements as representative sequences. To further explore the potential of pHMMs in such a search, we propose five alternative ways to obtain the sets of representative sequences of TEs other than the conventional protocol. In this study, we are interested in Bel-PAO, Copia, Gypsy, and DIRS superfamilies from the retrotransposon class. We compared the pHMMs of all six protocols. The test results show that, for each TE superfamily, the pHMMs of at least two of the proposed protocols performed better than the conventional one and that the number of correct predictions provided by the latter can be improved by considering together the results of one or more of the alternative protocols. (AU)

• Processo FAPESP: 11/00428-5 - Identificação de Elementos Transponíveis usando Modelos Ocultos de Markov
• Beneficiário: Victor Hugo Barella
• Modalidade de apoio: Bolsas no Brasil - Iniciação Científica
• Processo FAPESP: 12/22205-0 - Modelos ocultos de Markov aplicados a elementos transponíveis
• Beneficiário: Victor de Abreu Campos
• Modalidade de apoio: Bolsas no Brasil - Iniciação Científica
• Processo FAPESP: 12/24774-2 - Aplicação de Modelos Ocultos de Markov a elementos transponíveis
• Beneficiário: Carlos Norberto Fischer
• Modalidade de apoio: Bolsas no Exterior - Pesquisa